mirror of
https://github.com/MillironX/singularity-builds.git
synced 2024-10-22 12:13:08 +00:00
63 lines
1.5 KiB
Modula-2
63 lines
1.5 KiB
Modula-2
Bootstrap: library
|
|
From: default/debian:buster
|
|
|
|
%post
|
|
# Declare version variable
|
|
export SNIFFLES_VERSION='1.0.12'
|
|
export SNIFFLES_TAG="v${SNIFFLES_VERSION}b"
|
|
|
|
# Install dependencies
|
|
apt-get update
|
|
apt-get install -y --no-install-recommends \
|
|
git cmake make gcc g++ libghc-zlib-dev bash procps build-essential
|
|
|
|
# Get Sniffles
|
|
cd /opt || exit 1
|
|
git config --global http.sslverify false
|
|
git clone https://github.com/fritzsedlazeck/Sniffles.git
|
|
cd Sniffles || exit 1
|
|
git checkout $SNIFFLES_TAG
|
|
|
|
# Build Sniffles
|
|
mkdir build && cd build || exit 1
|
|
cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local
|
|
make
|
|
|
|
# Install Sniffles
|
|
cd ../bin/sniffles-core-$SNIFFLES_VERSION || exit 1
|
|
install -D -m 0755 sniffles -t /usr/local/bin
|
|
install -D -m 0755 sniffles-debug -t /usr/local/bin
|
|
|
|
# Cleanup repo
|
|
cd ../.. || exit 1
|
|
rm -rf Sniffles
|
|
|
|
# Cleanup packages
|
|
rm -rf /var/lib/apt/lists/*
|
|
|
|
%test
|
|
command -v bash
|
|
command -v ps
|
|
command -v sniffles
|
|
command -v sniffles-debug
|
|
|
|
%runscript
|
|
sniffles "$@"
|
|
|
|
%labels
|
|
Author 25492070+MillironX@users.noreply.github.com
|
|
SoftwareVersion v1.0.12b
|
|
SingularityDefinitionVersion 3
|
|
|
|
%help
|
|
Sniffles
|
|
========
|
|
|
|
Sniffles is a structural variation caller using third generation sequencing
|
|
(PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using
|
|
evidence from split-read alignments, high-mismatch regions, and coverage
|
|
analysis.
|
|
|
|
For more help, see
|
|
- <https://github.com/fritzsedlazeck/Sniffles>
|
|
- <https://github.com/MillironX/singularity-builds>
|